FWIW I'm on Linux Mint (Cinnamon, but I used to use MATE, maybe 6 months ago) ... and I don't have this issue.
The only (kinda) related thing I have noticed is that sometimes when I switch between EQ and something else, the ALT key gets sort of stuck, and I have to press it again to get it unstuck (but until I figure that out I'm like "why is pressing my #1 hotkey casting a spell"?).
But that doesn't really help you. Maybe try playing with wincfg and switching to/from virtual desktop mode?
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